Code: Alliance (Chapter 2)
by Chris Carver
Summary: After graduating, The Lyoko Warriors have to face off against Franz Hopper's former assistant: Professor Tyron. They also realize that X.A.N.A. yet lives on. With new teammates, will the heroes be able to defeat this new adversary and an old one? Find out in this exciting conclusion to my Code: Alliance Series.
1. Chapter 1

**Code: Alliance (Chapter 2)**

**Immediately after graduation, the Lyoko Warriors have gained a new enemy: Professor Tyron. Now with the help of two new friends, will the Warriors be able to defeat their new adversary? Find out in the exciting conclusion of Code: Alliance.**

**Disclaimer: I do not own Code Lyoko, its vehicles or characters. I do own Christopher, Chelsea, DJ, Jordan, Brady, Jacob, and Colton (one of the two new teammates).**

**Author's Note: The Skidbladnir and Megapod will be involved in this story. And they both will be big enough for all ten fighters.**

**Chapter 1: A New War**

_Christopher's POV_

"So, let's review: this guy betrays your dad, obtains his research through your mom, and now wants us dead?" Ulrich asked, earning nods from me and my sister. "And he has his own warriors that will attempt to do us in?" Odd added, again making me and Aelita nod. "Great. So now we have a new opponent to deal with." DJ said. "Yep. That about sums it up." I said. "Still, it's nothing we can't handle." Aelita said, earning support from me. "Aelita's right. We've been through worse." I said. "They're sure to study our moves in order to beat us." Yumi said, earning support from the rest of us. We then heard a knock at the door. "I'll get it." I shouted, changing back to my normal clothes. I went to the door and saw a blonde haired girl and a young man about her height with her. "Colton?! What are you doing here?!" I asked, demanding to know why my old rival was at my house. "Laura and I thought we could help you guys against your enemy." He said, nodding towards the girl that stood by her side. Aelita must've come by at some point, because I turned around and saw she was as furious as I was. "Why should we allow you to help us?" She and I said at the same time. "We're about as smart as you two, Jeremie and Chelsea, and your parents when it comes to computers." Laura said. Everyone else in the house invited them to come in, making me and my sister snarl. Our dad came up with Mom, and the two geniuses from the underground lab and saw Laura and Colton with the others. The two visitors explained that they wanted to help , and our father said yes. "WHAT?!" Aelita and I shouted at the same time. "Think about it, kids. What if something goes wrong in the lab? We could use all of the intelligence we can get." Our dad said, making Laura and Colton smirk at us. "How are the vehicles coming along, Papa?" I asked him, finally letting go of my distrust over Colton. "The ship is finished, but the Megapod is still not done yet." He replied. "We can help if you want." Laura said, earning a nod from Dad. As Colton came up to me, I grabbed his arm and Aelita grabbed Laura's. "If you two even think about flirting with Chelsea and Jeremie, we will throw you both out in a heartbeat, clear?" We both said, earning nods of fear from the both of them. "Good. Now go on." We both said, looking at each other after they were gone and chuckled at the fact they thought we would actually kick them out. "I suggest we bury the hatchet with them." I said, earning a nod from her. We all then went to the elevator that led to the lab and saw the four geniuses at the computer with our mother putting some additional touches on the Skid. While the others went to admire the ship, Aelita and I walked over to Laura and Colton. "Bygones?" We both asked, extending our hands. Laura and Colton nodded, shaking hands with us. "Done. The Megapod is finished." Our dad said, making everyone cheer. Just as he said that, the alarm went off. "Looks like we'll get to test out one of our toys soon enough. Check this out." I said, turning on the news to reveal the Ninjas were back and ready for action. The ten of us got ready for action. "Transform to Warrior!" We said, activating our Lyoko uniforms. We hopped into the Megapod and rode it into the city.

_General POV_

While the Ninjas were wreaking havoc, the Warriors arrived ready to fight. "Miss us, Ninjas?" Christopher asked. "Not really." The red Ninja said. "Wow. I fight a chick." Christopher said, astonished that the lead Ninja was a girl. "Doesn't matter. We can still fight them." Aelita said. "Then let's do this." Odd said. They took a fighting stance and then attacked. The Warriors and Ninjas all seem evenly matched for the first fifteen minutes. After another fifteen minutes, the Ninjas retreated. The Warriors were on their way back to the lab when a reporter that was on the scene asked what they wanted to be called. "Call us the Lyoko Warriors." Christopher said as he loaded up in the Megapod and they all drove away. When they arrived back to the lab, the news was replaying the footage from their fight. "Wow. We rock." Odd said, earning nods from everyone in the lab. "One thing is certain: We have a new war to fight." The Schaeffer twins said at the same time.

**That's chapter one. Despite the fact that I was a fan of the rivalry Aelita and Laura had, I thought it would create too much of a problem for the team. So I decided for them to make amends in this story. Review and I'll post more chapters.**


	2. Chapter 2

**Chapter 2: Tracking and Spying on the Enemy And A Dark Secret Revealed**

_Aelita's POV_

I woke up to the alarm and saw I was asleep on my brother's lap. He also woke up as did the others. We were all exhausted from our battle with the Ninjas the night before and wanted to get some sleep. I quickly sat up and was as embarrassed as he was when he saw on his lap. The ten of us went from the living room of our house to the underground lab only to find out there was no attack, which made all of us a little mad. "Why did the alarm go off if the Ninjas aren't attacking?" Christopher asked. "We might have a way to find out where their base is." Laura said. "So the alarm was the best way to get us up?" I asked. "We tried to wake you guys, but you all just refused wake up." Jeremie said. "Great thinking. Next do something less painful like dump ice cold water on us." Odd said. "Anyway, after you guys went upstairs, we decided it would be a good idea to find out where Tyron's base of operations is. So the five of us stayed down here and came up with this." Colton said, revealing some kind of tracking beacon. "The only catch is it has to be placed on the Red Ninja's back." Chelsea said, looking to my brother. "All right. I'll do it." He said, knowing the Red Ninja had it out for him. "First, you'll need her to find you, then, once you get behind her, place the tracking beacon, then just get out of sight. She'll surely give up after you 'disappear'." Chelsea explained. "Seems easy enough. But why stop at finding Tyron's base? Why not spy on him too?" Christopher asked. "I don't see why not. The only problem is it's bound to be heavily guarded." Laura pointed out. "Ah, right. Well, it's a good thing I created and added a stealth mode to all of our suits." My brother said with an sneaky smile on his face. "You are sneaky." I told him. "I learned from the best." He said, looking to Brady and Odd. "If the other Ninjas show up, we'll keep them off him so he can plant the tracking device on the Red Ninja." Ulrich said, earning a nod from the rest of us. "Okay." Daddy said.

[ALARM BLARING]

"Looks like it's showtime." I said. The ten of us changed into our uniforms and headed for the Skid. Our dad energized us into the ship, then released the supports. Once they were released, we took off into the city. We docked the Skid and disembarked from it. We attacked our designated Ninjas while my brother dealt with the Red Ninja.

_General POV_

"So, you came to play." The Red Ninja said to the Red Warrior. "You might say that, sweetheart." He retorted. The two red fighters then engaged in hand-to-hand combat. After a few minutes, Christopher vaulted over the Red Ninja and shoved her, placing the tracking beacon on her in the process. After it was done, the Warriors looked to Christopher to see him the signal that the beacon was in place. The Warriors then reenergized back into the ship and flew away. With that, the Ninjas returned to Tyron. The Skid returned to drydock and the ten fighters disembarked from the ship while it was docking. "The beacon's in place." Christopher said. "Good. Now, let's turn it on." Franz said, activating the tracking device. "Wow. He's in Switzerland." Laura said." The twins looked to Anthea. "Isn't that where you were being held prisoner?" Aelita asked, earning a nod from her mother. "I'm gonna kill him." Christopher said. "Easy boy. We can't just waltz in and kill everyone in sight." Ulrich said. "He's right. We have to be discreet about it." William said. Christopher conceded and nodded his head in agreement. "Your stealth program will make you guys completely invisible to Tyron's surveillance, but not each other." Franz said confused. "I designed it that way. Just in case we need to use the hand signals we use in combat." Christopher then went on to explain the whole concept to everyone. "In English." Odd said. "It means that, to each other, we'll appear holographic. But to Tyron, we'll be completely invisible." Aelita translated. "Exactly." Christopher said. "I also added it to the ship, the NavSkids, and the Megapod." He added. "You're only choice for transport right now is the Megapod. The ship needs time to refuel." Jeremie said. "How long will it take?" Yumi asked. "12 hours." Jeremie said. "Okay. The Megapod it is, then." Christopher said as Odd hopped in the driver's seat. The others piled in and Christopher activated the stealth mode for the ride and showed the others how to activate it. After that, they rode to Switzerland.

_A few hours later_

_Odd's POV_

I was still awake since I was driving when I looked and saw the others were asleep. "Wow. It's gonna be a long drive." I said to myself. I then got back on track and drove to the complex. A few more hours of driving and we arrived. I woke the others up. "Okay, now seeing as how Tyron keeps all of his guards, except the Ninjas, at the front gate, someone's gonna have to set off an explosion so we can get through unseen." Christopher said. "Great. Only how do we do that?" I asked him. "We still some of those explosives from when we blew up the factory, right?" He said, and we all knew what he had in mind. We pulled out the explosives and set them inside a bunch of old cars not far away. I took charge to detonate them. "On my signal, Odd." Christopher said to me via the Transwatches. "Roger, boss." I said. "Three... Two... One... Now!" He said and I pushed the button and set off the explosion. Just as Brother Einstein predicted, the guards, and Ninjas went to investigate the explosion. The ten of us made our way through the complex and found Tyron's lab. Brady took the spy camera and placed it where it would not be easily seen. He finally found a place that was perfect and placed the camera in position. After that, we got back to the Megapod and drove all the way back to the Hermitage. I put the Autodrive feature on and decided to join the others in a little nap. We made it back a few hours later and didn't wake up so, the others left us in the lab to sleep.

_The next morning_

_General POV_

The ten Warriors woke up and realized they slept the entire return trip to the lab. "Wow. Have we been asleep long?" Christopher asked. "The entire night, actually." Franz said, coming down to the lab to check on them. "The camera? Is it in place?" Aelita asked, and her father nodded his head. "Good. Hey, check this out guys." Yumi said, pointing to the screen connected to the camera. The others came by to see the live feed and were shocked to find out that the Red and Pink Ninjas were Tyron's children. His daughter was the Red Ninja and the Pink Ninja was his son.

**That's chapter two. When I was writing this, I was toying around with the idea of if Tyron had twin children. I'm still working out the rest of the details for this story but I hope you guys enjoy the story and where I'm going with it so far. Review and I'll post more chapters.**


	3. Chapter 3

**Chapter 3: An Old Enemy Returns and Meeting with the Enemy**

_Aelita's POV_

_I was on Lyoko with my brother and our friends, fighting the Ninjas when all of a sudden, an all too familiar screech is heard: The screech from the Scyphozoa. Christopher and I turned around and saw not one, but two of the monster. We both got really scared and tried to run, but we couldn't. Our feet were frozen like the floor of the Sector we were in. Suddenly, the ends of the monsters' tentacles then extended blades. As soon as all of the blades came out, we were stabbed and killed. We screamed and then everything went black._

I screamed and woke everyone in the lab up. Christopher came over to ask me what happened. I then explained my nightmare to him. "Don't worry. X.A.N.A.'s been defeated. He can never come back." He reassured me as the others came to us after hearing me talk about my nightmare. "He's right. It's impossible for him to still be alive." Jeremie added. "Plus, I don't want to fight X.A.N.A. for a third time." William said, earning agreements from everyone, including me. Then the alarm went off, signaling the Ninjas were back and on the offensive. Luckily, we were already in our Lyoko forms and ready to fight. Me especially because I had to get my mind off my nightmare. We hopped in the Skid and flew into the town. We arrived to where the action was, but were scared stiff by what we saw instead of the Ninjas: A Megatank. "So much for hoping never to fight him again." I said. "Who cares? It'll join its friends in destruction." my brother said, frustrated by the monster that was wreaking havoc in the streets. I disembarked him and he attacked the overgrown bowling ball with anger. He destroyed it and then, the Ninjas arrived. We all then dis embarked and joined him in battle. "How's Daddy?" He asked, clearly wanting to agitate Tyron's daughter. "Let's go see him." She said, clearly in the mood for a fight. He charged her and she charged him and they fought hand-to-hand. We all then dealt with the other Ninjas.

After about half an hour, the Ninjas retreated. We went back to the Skid, wanting to see how Tyron would react, and demanding answers as to why a Megatank was terrorizing innocent lives. "How is he still alive?!" I asked, even more furious than my brother. "I don't know, Aelita." Jeremie said, as confused as we were angry. "He might have survived by an unknown method." Laura said, "Thank you for stating the obvious, Laura." I said. "Calm down, sis. There's no need to get worked up. Just because you had a nightmare about X.A.N.A. doesn't mean we'll die." My brother said, getting me to ease up a bit. I finally settled down and apologized to Laura. She accepted my apology. "I just found another virtual world in the Network. I've also picked up activity there too. It's data. It's quantum." Our dad explained. "Like the one of yours?" Christopher asked. "Not LIKE the one of mine. It's the same. Exactly the same." "Then, how do we get there?" I asked, wanting to finish off X.A.N.A. so we could focus on Tyron. "Fortunately enough, your Transwatches also serve as virtualizers that you can use to get to a virtual world. In this case, this Cortex, as we'll call it. You just have to say 'Virtualize' and then you say the place you want to be virtualized to." Our dad explained. "Virtualize, Cortex." Odd shouted. Within a few seconds, he was gone. "Dork." Ulrich said. "Hey, you're the one who had to share a room with him." I said. "By the way, Odd. How'd you manage to get Kiwi out of the school?" Christopher asked. "Simple. I just stuffed him in my bag until I was near the Hermitage." Odd replied as he came back to the lab. Christopher nodded in understanding. "Guys, take a look at this." Chelsea said. We all came over to see Tyron yelling at his Ninjas.

"Why did you not kill these Lyoko Warriors again?!" He asked. "We're sorry Daddy. We've tried but they're just too strong. They can match our moves no matter what we do." The Red Ninja said. "Try harder, Alice. You're getting defeated by a boy who looks like an elf!" Tyron said, clearly getting furious. "Unless you're beginning to develop feelings for him." Tyron inquired, which his daughter quickly denied. "Like you said, he looks like an elf." Alice added after denying her father's inquiry. He then looked to his son. "And you, James? Are you developing feelings for that pink elf?" He asked his son, who also denied the inquiry, just like Alice did. "And you, Raven? Are you developing feeling for that green cat?" He asked, with the Green Ninja, Raven, denying the inquiry as quickly as the twins. "Angel? Are you developing feeling for that silver warrior?" He asked, with the Silver Ninja, Angel, denying the inquiry as quick as the other three. "Good. Now next time, and this applies to all of you, KILL THOSE LYOKO WARRIORS!" He shouted, making them all flinch, but nod their heads in fear. "I think the Red Ninja, Alice, might be developing feelings for me. I have noticed she hesitates before she attacks me." Christopher inquired, explaining how her fighting style was compared to his. "I noticed her brother hesitate to attack me as well." I added. Brady and Jacob also pointed out how their opponents, Raven and Angel, hesitate when they're fighting them as well. "And the four of them denied it pretty quickly. I suggest you guys offer to meet them in order to find out. Ask them to come with just the four of them. I suggest you go with each other as well. And don't reveal to them that we have a spy camera set up in Tyron's laboratory." Colton said, earning a nod from my brother."We'll be on standby, just in case." I offered, and the other two agreed. With that, we used the Overbike and Overwing and rode into the town until we found a news reporter. "I need to send a message to someone, and I need a camera to do it." He said, earning a nod from the reporter and her cameraman. "Hello. I am the Red Lyoko Warrior. These are three of my teammates. We have a message for the Red Ninja, the Pink Ninja, the Green Ninja, and the Silver Ninja: We want to talk to you about something. Meet us in the park in here outside our town six hours. And do not bring any more of your companions. We will not fight. I repeat, do not bring any of your other companions with you. If you do, we will fight them."

_Meanwhile, in Switzerland_

_Alice's POV_

I saw the Red Lyoko Warrior's message and decided I would take James, Raven, and Angel with me, so I told them about the meeting request the Warriors offered us and made them swear not to tell my father. They agreed and we went off to find a news reporter and cameraman to tell the Warriors we accepted their request. "We want to say something to the Red Warrior, the Pink Warrior, the Green Warrior, and the Silver Warrior. And it is: We accept your meeting request and will be there soon, but no one else will come. I give you my word." I stated. And with that, I activated my super speed and headed to the rendezvous with James, Raven, and Angel hot on my heels. We made it to the park the Warrior suggested and saw him and the other three Warriors were standing there waiting for us. I told James, Raven, and Angel to stay where they were, but remain wary. With that, they went and stood next to a tree with the other three Warriors moving to the same tree they went to.

_General POV_

"First off, I don't believe we properly met. My name is Christopher. The Pink Warrior is my sister, Aelita, the Green Warrior is my friend, Brady, and the Silver Warrior is my other friend, Jacob." Christopher said, introducing himself, his sister, and his friends. "I know. My dad told us everything about you. My name is Alice and that is my brother, James and our friends, Raven and Angel." Alice said, not at all sounding rude, and introducing herself, her brother, and their friends. "It's nice to meet you, Alice, and you as well, James, Raven and Angel. And if you touch my sister, James, I'll kill you. Same goes for you two. Anyway, Alice, I've noticed you hesitate when you and I fight. They noticed the same thing when they fight us. I got to wondering. Why is that?" Christopher asked, getting back to the purpose of the meeting. "I don't know. I just think you're kind of handsome." Alice said, admitting her feelings for the red haired elf a little. "Well, then. I'm sure your father gets mad when you head back in defeat." "Yeah, he yelled at us just today as a matter of fact. He even asked if I had feelings for you, which I denied because I knew he would kill me if I said yes. So I got to wondering if all of this was worth it if all my father wants is revenge for your father firing him. He captured your mother and tortured her until she gave him your father's archives. I'm beginning to doubt that I want to fight for my father, who was driven to becoming a mad scientist in order to get back at Franz Hopper." Alice explained why Tyron was doing what he was doing. "You know, if you and your team are unhappy fighting for your father, we could use some more hands. Our house always has room. Right, Aelita?" Christopher said, looking to his sister. "Absolutely. You and you team could come with us and explain everything to our father. He'll welcome you guys with open arms." Aelita added, knowing they weren't fighting the Warriors of their own free will. "Thank you, guys. We just might take you up on that offer." Alice said, with James nodding his head. "We'll need a way to contact our teammates." James said, which gave Christopher an idea. "Here, use this, Alice." Christopher said, handing her her own Virtualizer. "Thanks." Alice, James, Raven, and Angel said, indicating that Aelita, Brady, and Jacob gave them their own. The Warriors then handed the four Ninjas six other Virtualizers for their teammates. The elven twins then explained to the Ninjas how they worked and the commands they could use.

_A few hours later_

_Alice's POV_

We arrived at the Hermitage with our teammates, without telling my father, and knocked on the door. "I'll get it!" I heard someone shout and guessed it was Christopher. The door opened and I was right. He, Aelita, Brady, and Jacob then led us down to Franz Hopper so we could explain our predicament to him. "I gotta warn you guys. Our friends don't know you guys are joining our team. So give them time. They'll adjust eventually." Christopher said. "We also designed you guys your own ship and Megapod like ours except in colors you guys might like." Aelita explained. "We also have three other vehicles for you guys." Brady and Jacob said at the same time. All fourteen of us then arrived in the underground lab and saw the samurais, geishas, cats, and warriors and got nervous when they saw us. They almost attacked us when the elf twins stopped and explained everything I told Christopher. We then all went to Franz and explained our situation to him. And his son was right. He accepted us with open arms. Next time we would fight, it would be side-by-side.

**That's chapter three. I'm also deciding whether or not I want a romance to brew between the Warriors and the Ninjas. If you guys think I should, let me know. Next chapter will be a real shock. Review and I'll post more chapters.**


	4. Chapter 4

**Chapter 4: A Shocking Discovery**

_Christopher's POV_

We were in the lab with the Ninjas when Ulrich pulled me out of earshot. "What were you thinking bringing them here?" He asked me. "Ulrich, you saw how Tyron was to them. And besides, they're not that bad and now that X.A.N.A.'s back, we need all the help we can get. Just give them a chance." I said. "Why should I?" He asked, making me angry. "If you don't, then I'm afraid I'll have to kick you out. I have no choice." "The only way I'll accept them is if Matt saves my life. That's what I did with William." Ulrich said and then explained to me how William saved him from falling into the Digital Sea. "Well, Lyoko's gone, okay? So there are only two places he can save your life. Either here or on the Cortex." I said to him just before the alarm went off. All twenty of us hopped into our Megapods and rode into the town. We arrived and could not believe our eyes. A Tarantula and a Ninja were standing side by side. "Okay. That is not a good sign. If those two are side by side, then that means that Tyron and X.A.N.A. are working together." I said. "Alice, you and the others handle the Ninja. We'll take care of the Tarantula." Aelita said. "Got it." Alice said as we all disembarked and attacked. The Tarantula was destroyed when I looked and saw Ulrich was about to die. Fortunately, Matt ran and stopped his sword from striking the samurai. Matt then fought him as Ulrich got back on his feet. He then thanked Matt for saving his life and the Ninja left for Switzerland. "Looks like your dad has caught onto your betrayal, guys." I said to our new teammates, earning nods from them. "We should head to the Cortex. Just to make sure X.A.N.A. didn't activate a tower to send in that Tarantula." James suggested. "Papa?" I said, hoping he heard what James just said. "I heard him, son. And I agree completely." He said. "Virtualize. Cortex." We all shouted and ended up on the Cortex.

Suddenly, a weird sound was heard and me and Aelita doubled over, covering our ears and screaming in pain. "What's that noise?" Yumi asked. "It's the alarm. It indicates that there are intruders on the Cortex. In this case: us." Alice said. "What's wrong with them, then?" Odd asked, pointing toward us. "It must have something to do with the fact that some of their computer DNA lingers in their bodies." Jeremie said from the underground lab. As soon as the noise stopped, my sister and I stood up straight. "Wow. Try sampling that, sis." I said, feeling very lightheaded. "You first." She retorted before everything went black.

_General POV_

The others saw the elven twins unconscious on the floor. "It'll take them some time to adjust. But I'm sure they will eventually." Alice said as Tina helped get Christopher onto her back. "Follow us. We know this place and its most discreet hiding places." James said after Jon helped do the same thing to Aelita. With that, they all made their way to the tower to find it inactive. "Your dad must've written a program that X.A.N.A. can use to materialize his monsters." William said, earning agreements from the others. "There's a way to be certain. We have to get to the Core of the Cortex." Alice ordered. "Hopefully, Christopher and Aelita come wake up by the time we get there." Kat said. They all then made it to the giant sphere that Tyron's children said was the Core of the Cortex. As soon as they arrived, the two unconscious elves started to wake up. "Wha- What happened to us? And why am I on Alice's back?" Christopher asked. Alice set him down and James did the same thing to Aelita and the twin Ninjas explained what happened to them as soon as they arrived onto the Cortex. "Hopefully, we will adjust to it." Aelita said. "So, if I understand this correctly, we need this door opened, correct?" Christopher asked, earning a nod from Alice. "Aelita, come help me." He ordered. She obeyed and mimed her brother's movements. Before long they were glowing blue, indicating they were using their Creativity. The door then opened up and Alice instructed the others to follow her. They all then went to a teleporter.

_A few seconds later_

_Aelita's POV_

Next thing we knew, we all ended up in a strange room. "Incredible. This place is hallucinating." William said. "Yeah. I've never seen anything like it." Jacob said. I then looked toward Alice and saw her look around until she found what she was looking for. "Down there. That's our father's terminal." She said, getting everyone to look in the direction she was pointing. "Let's go. Oh, and mind the walls. They'll start coming out in a few seconds." James said. My brother and I activated our wings and flew to the console while William and Jacob used their Supersmoke to catch up to us. "Unfortunately, we can't access it so easily." Alice said. "Leave it to me." I said, placing my hand in the terminal. A screen came up then a live feed from a webcam popped up and we were shocked by what we saw: Tyron, in an all purple Ninja suit, creating a robotic body we presumed was being made for X.A.N.A. "Guys, did you get the data?" I asked the others in the lab. "Yeah. Come on home, guys." Jeremie said. We all then shouted "Devirtualize" and ended up back in the lab, scared at what we had just seen. "Our greatest battle is yet to come." I said, earning agreements from everyone else in the lab.

**That's chapter four. Before I started typing this chapter, I got to wondering "What if Tyron and X.A.N.A. were working together?" So that was the shock I threw into this chapter. Will the heroes be able to destroy X.A.N.A. and defeat Tyron? Find out next few chapters. Review and I'll keep posting more chapters.**


	5. Chapter 5

**Chapter 5: A New Plan**

_Christopher's POV_

We were all in the lab, trying to come up with a new plan to get rid of X.A.N.A. "Another multi-agent system?" Jeremie asked. "Yeah, because that worked out just fine last time." I said with sarcasm in my voice. "I don't see you coming up with any ideas." Jeremie retorted, making me want to walk up and punch him in the face. Alice stopped me while Chelsea stopped Jeremie. Jeremie stopped while I kept walking towards him. Then, Alice did something that surprised everyone, including her. She leaned her head towards mine and planted her lips on mine. I was in shock by her reaction that I couldn't even move a muscle. She then removed her lips from mine. "Why'd you do that?" I asked her, confused and blushing. "To get you to calm down." She replied with an innocent look on her face. "So, the multi-agent system is out of the question. Anything else in mind?" Aelita asked. "What about a virus?" James suggested. "That just might work." I said. "Then it's settled. We will use a virus to kill X.A.N.A. once and for all." Chelsea said. "Now that that's done, what are we going to do about my father?" Alice asked, causing me to look at my own father. "Papa, do you think we could use a special Return to the Past for Tyron so that he won't remember a thing? But just for him and only him?" I asked, making him look towards Alice. "I could do that, seeing as how you don't want Alice to forget who you are." He replied, making me blush even more than when Alice kissed me. "Unfortunately, and I know you and Aelita aren't gonna like this Christopher, you guys have to gather data from the Cortex." Chelsea said, making me and my sister shake in fear. "Don't worry. We'll do it just like we did last time." Alice told me, reassuring me by putting her hand on my shoulder with James doing the same thing to Aelita. "Let's go then." I said, knowing what would happen to me and Aelita when we arrive. "Virtualize, Cortex!" We all shouted and Aelita and I braced ourselves.

_General POV_

The alarm on the Cortex went off, causing the Schaeffer twins to scream in pain, then pass out after the alarm stopped. Kat helped Alice get Christopher onto her back while Tom helped James get Aelita onto his back. Everything on the Cortex then started moving. "We'll have to work fast." Alice said as she started running with the others in tow. When they reached the Core, the elven twins came to. "Wakey wakey, sleeping beauties." Alice joked, making James laugh. Christopher and Aelita got down from Alice and James's backs, but couldn't stand up straight. "Let's wait until they get their footing back." Ulrich suggested. After a few minutes, the twins got their footing back and made their way to the door, placed their hands on it and began to glow blue, signaling the use of their Creativity, and opened the door. The twenty of them were then teleported to the core room.

_Aelita's POV _

We arrived into the core room and my brother and I activating our wings and flew down to the interface while Jacob and William used their Supersmoke to join us and Alice and her team used their phasing abilities to catch up with us and the others used the platforms to get to where we were. I inserted the virtual card and the data was starting to download when Tyron and X.A.N.A. showed up. "Alert. Intruders in the core room. Immediate virtualization." Tyron said before he and X.A.N.A. walked away. "Get ready you guys. Tyron and X.A.N.A. are calling up their troops." Jeremie said. "Yeah. We can confirm that." I said as monsters and Ninjas appeared. "Guys, protect the interface at all costs. We absolutely have to get that data." Chelsea said. "Roger, Chelsea." Christopher said as we fought the monsters while Alice and her team engaged the Ninjas. After a few minutes, we heard the guys in the lab. "Guys, they're too strong. We have half of the data we need. The rest is gonna have to wait until next time. Come home you guys." Daddy said. "Okay, Daddy." I said as I went and removed the virtual card. "Materialize, Lab." We all said and rematerialized back into the lab. "Save your strength, guys. There'll be another time." Mom said. After that, we all decided to get some rest and found scattered parts of the lab and fell asleep.

**That's chapter five. I'm sorry it took a while to post. I've been busy with my two other fanfics I'm working on and another just came to me. I've also been fighting writers block. I forgot to mention in the last chapter that there were still some traces of artificial DNA left in Christopher and Aelita. That's why they passed out in the Cortex in the last chapter and this one. But by the end of the story, they'll get used to it. Review and I'll post more chapters.**


	6. Chapter 6

**Chapter 6: A Deception**

_Aelita's POV_

"We have to go back to the Cortex and gather the rest of the data for making the virus to kill X.A.N.A." Alice said, earning agreements from the rest of us. "Then what are we waiting for? Let's go." I said. We all then virtualized onto the Cortex and, as usual, my brother and I braced ourselves. As soon as the noise stopped, we both blacked out.

_Alice's POV_

James and I were about to do our usual thing and put the elven siblings onto our backs, but this time, our father had sent other Ninjas to stop us. The rest of us tried to fight them off, but they were too strong. After what seemed to be a pointless battle, we were defeated, but not devirtualized. We were out cold for a few minutes and I was the first one to come to. As soon as I was back on my feet, I looked for Christopher and his sister, but saw they were nowhere in sight. I got the others up and told them that Aelita and Christopher were nowhere near us. We then spread out and searched different parts of the Cortex.

_With the elven twins_

_General POV_

"Is it ready yet?" Tyron asked, quickly getting impatient. "Almost. Just a few more calculations. And done." X.A.N.A. replied with an evil grin on his face. "Good. Now head to the core room and inject them with the virus." Tyron said. X.A.N.A. then virtualized himself into the core room and injected the unconscious elves with the mind control virus, leaving Tyron unaware that it was really a Made in X.A.N.A. virus that will turn them. "Done." X.A.N.A. said as James and Alice made themselves known to the both of them. "I'll distract X.A.N.A. while you get Aelita and Christopher out of here." Alice told her brother and he nodded. She then drew her sword to fight against X.A.N.A. While X.A.N.A.'s back was turned to James, he took the opportunity to save the Schaeffer twins. As soon as he was on the teleporter with them, Alice followed behind him, but X.A.N.A. did not. "Jeremie, we got 'em." Alice said. "Great. We'll tell the others to meet up with you guys at the tower. They have to regenerate themselves." Jeremie said as James and Alice saw their teammates were waiting to head to the tower to meet up with the Warriors.

About an hour later, they reached the tower. "James and I will take them in." Alice said, feeling guilty for not reaching the elf that she loved in time. They both then entered the tower then left after setting the elven twins down in the center of the platform. Once they were outside the tower, James and Alice explained all that happened in the core room. "They have half their life points now." Jeremie said as everyone else began to get the felling that something wasn't right, James and Alice especially. "You guys said X.A.N.A. was in the core room, right?" Jordan asked, earning nods from the both of them. "Did he try to follow you?" Yumi asked, resulting in James and Alice shaking their heads no. "Jeremie, we have to get them out of the tower." Kat said. "Why, Kat? They don't have all of their life poi- Yes! They have all of their life points back." Jeremie said. "Jeremie, I don't think you should celebrate." Tina said just as the tower turned purple. "Oh no. Tyron has just activated the tower." Chelsea said. "Don't sweat it. One of them can deactivate it, right guys?" Jeremie said. "Right." The two in the tower said. Just then, the tower turned red. "What? Guys, looks like X.A.N.A. has taken control of the tower." Laura said. Just as she said that, the elves came out of the tower, Christopher in a blue version of his outfit and Aelita in a purple version of her outfit, with the sign of X.A.N.A. in their eyes. "Now we know why X.A.N.A. didn't follow us." James said. "Dad's not gonna be happy about this." Alice said. The Xanafied twins then attacked the others then headed for the Dome at their new master's request.

They made it to the Dome and were teleported to the core room just in time to see Tyron prepared to yell at X.A.N.A. "What have you done to them?! They should be dressed like Ninjas!" He shouted as soon as the new X.A.N.A. Warriors arrived. "Did you think I would give control of Franz Hopper's children to you? Did you think I would even work with you? It was all a deception." X.A.N.A. retorted, laughing evilly in the process.

TO BE CONTINUED...

**Will the Lyoko Warriors and the Cortex Ninjas be able to save their allies from the maniacal program's clutches? Find out in the first of the two part ending of Code: Alliance. Review and I'll post more chapters.**


	7. Chapter 7

**Chapter 7: The Final Battle part 1**

_Alice's POV_

"We have to save them." I said. "We will, Alice. But in order to do that, we will need the rest of the data we need for the virus." Jeremie said. "Chris and Aelita are sure to stop us." DJ said. "Kat and I can keep them busy." Tom said, earning a nod from his teammate. "Okay. We're sending you guys the card that has half the data we need for the virus to you. Jordan, hold out your hand." Chelsea said, and Jordan obliged. "We aren't that far from the Dome. Let's go." James said as he began running at top speed with the samurais and his fellow Ninjas in tow. William and Jacob use their Supersmoke to keep up while the geishas and cats hopped onto their vehicles.

_General POV_

Eventually, they all made it to the Dome to find the door was open. They went inside and made it to the core room to find the Xanafied elves were waiting for them. Kat and Tom drew their swords and prepared to attack. They held off the twins while the others dealt with the other Ninjas and Tyron dealt with X.A.N.A. for his treachery "Chelsea, the card is in place." Jordan said. "All right. We'll let you know when we have all of the data. Matt, Tina, you guys might want to help Tom and Kat." Chelsea said, causing the two Ninjas to look and see that their teammates were getting pounded. "We're on it." Matt said as he and Tina drew their swords. "Don't hurt them." Alice said. "No promises." Tina said as they went to help Tom and Kat. "Need a hand?" Matt said, earning a nod from his brother as Tina ran to help her sister. "Just hanging out?" Tina joked. "Very funny. Now help me up." Kat said. "We have to be careful. They may be under X.A.N.A.'s power, but they're still our friends." Kat said as the four Ninjas attacked the two elves.

After about an hour, Chelsea spoke again. "Guys, we have all of the data we need to make the virus. We also have ten scanners in the lab and they're connected to the computer here in the lab. You guys better come back." She said as one by one, the Warriors and Ninjas were devirtualized, with James and Alice still fighting. "James and Alice, did you not hear what Chelsea said ? Get outta there." Jeremie ordered and the Ninjas reluctantly allowed themselves to be devirtualized.

_Back in the lab_

_Alice's POV_

"We need to set Christopher and Aelita free before we launch the virus." I said. "Alice, they weren't possessed by specters, but by a virus. I'm afraid they're now linked to X.A.N.A." Jeremie said. "Don't you guys understand?! I love him!" I shouted, much to everyone's realization, including my own. "And you, James? You love Aelita, don't you?" Chelsea asked, earning a nod from him. "We may have to put them in a medically induced coma in order for them to survive." I heard Aelita's mother say. I reluctantly agreed to it. "It's settled then. We'll set up the capsules for them." Franz said. I took off because I didn't wan anyone to see me cry. James came after me to cheer me up. "It won't be permanent, sis. We'll find a way to reawaken them. I promise." He said, giving me a new hope. "Okay." I said, drying my tears. After he left, I felt my heart gain a new sense of hope. "I will set you free, Christopher. I swear on my life." I said under my breath.

**Will Alice be able to save the one she loves? Find out in the exciting conclusion of Code: Alliance. Review and I'll post more chapters.**


	8. Chapter 8

**Chapter 8: The Final Battle part 2**

_Alice's POV_

I was in the lab with the others, still torn that Christopher would have to be put into a coma in order to survive. James saw me petting Kiwi while I was crying and came to comfort me. "What's wrong, Ali?" He asked me. "Why did this have to happen to them? I should've made it to him faster." I replied feeling terrible that I didn't reach the one I love quickly enough. Yumi came over as well to help my brother comfort me. "Alice, what happened to them could have happened to any of us. Don't blame yourself." She said to me, making me feel a little bit better. "She's right. Some things don't happen the way we expect. We will save them." James said, making me smile.

After a few hours, the capsules where Aelita and Christopher would sleep were set up and connected to life support systems. I sighed, with sadness, as I looked at them. I looked up and noticed a weird tube connected to the capsules. I called Franz over and asked him what it was for. "It will be how they will be able to communicate with each other." He explained. "Will he be able to hear me?" I asked, hoping he would give me a positive answer. "It's possible." He replied, and I thanked him, knowing there would be a way for me to communicate with him. "I know you're concerned, Alice. I am too, and so is Anthea. But I promise you, it will not be permanent. We will find a way to reawaken them." Franz said, giving me a new sense of hope.

_The next morning_

_General POV_

"The virus will destroy the Cortex and X.A.N.A. We've made a sedative for Chris and Aelita. It'll have to be injected into them. Any volunteers?" Chelsea asked and Alice volunteered to do it. "Ali, are you sure you want to do this?" James asked. "Yes. I'm the one responsible for losing them. So I'll inject them both." Alice replied as Chelsea handed her the sedative. "You'll have to stop halfway for Chris, then inject the rest of it into Aelita. Then, we'll launch the virus." She said as Alice took the syringe. "Good luck, guys." Jeremie said as they virtualized themselves onto the Cortex.

_While the team were on their way to the core room_

X.A.N.A. had made himself a throne and watched as his new Warriors were sparring with each other. Aelita raised her leg but her brother dodged it easily when X.A.N.A. saw Tyron was virtualized into the core room. "TRAITOR!" Tyron shouted as X.A.N.A. called his Krabs and Tarantulas to deal with Tyron's Ninjas. The team arrived to see an all-out war being raged between the monsters and the Ninjas. Christopher saw the team and he and Aelita attacked. "You guys take care of the monsters and the Ninjas, I'll save the twins." Alice ordered. "Not alone, you won't." James said as he stood by her side.

After a few hours, the monsters were all destroyed and the Ninjas were all devirtualized. All but Tyron, X.A.N.A., Alice, James, Christopher, and Aelita were at the terminal. Alice vaulted behind Christopher and injected him with half of the sedative. "Sorry, Christopher." She said as he fell to the floor. As she worked her way to Aelita, Christopher's outfit changed back to its original color. James held Aelita in place while Alice injected her with the rest of the sedative. After she was asleep, Alice ran to Christopher to see his outfit had returned to its original color and looked at Aelita to see the same thing was happening to her. "Guys, what do we do now?" She asked as Jordan injected the virus into the terminal. "Devirtualize Chris and Aelita and then rematerialize back here." Jeremie ordered as Alice and James stabbed the elves with their swords then rematerialized back in the lab. "Hurry! Get them into the capsules!" Franz ordered as the sleeping elves were put into the capsules and the tube connected to the backs of their necks. The Cortex was destroyed, X.A.N.A.'s body destroyed, and Tyron lost in the Network forever. The twins' life support systems activated and the heroes were relieved.

_With the Schaeffer twins_

_Christopher's POV _

"Ugh. Wha- Where am I?" I asked as I looked around to see that I was in Lyoko's Ice Sector. "What am I doing back on Lyoko?" I asked myself before I remembered what happened. I then grew concerned for my sister. "AELITA!" I screamed, hoping she was in the same location I was. "CHRISTOPHER!" I heard a voice shout and I realized it was my sister. I ran to where the source of the voice was coming from and saw Aelita. I smiled and ran to hug her. "What happened?" She asked me. "I don't know. The last thing I remember was me fighting Alice. It's a blank after that. That is until I woke up here in the Ice Sector." I explained. "Is it weird that no monsters have shown up?" She asked me. "Yeah, it is." I replied until I saw Dad. "PAPA! Why are we back on Lyoko?" I asked him. "Technically, you're not." He replied. Aelita and I rose an eyebrow. "Maybe Alice hit me in the head." I said, completely confused. "Yeah. How could we be on Lyoko, if we're technically not?" Aelita asked. "You both had to be put in a medically induced coma. Alice and James are working with me to try and reawaken you." He explained. "How long could it take?" I asked. "It's unclear how long. For now, be patient. We'll find a way to bring you both home." He replied. A tower appeared for us to wait in.

_In the lab_

_General POV_

"Did you tell them?" Anthea asked. "Yes, I created a tower for them to hide in while they wait." Franz replied. "Right. Let's get to work."

**Will the heroes find a way to bring their fearless leaders home? Find out in the bonus chapter. I decided that I wouldn't use a Return to the Past to erase Tyron's memory. I'm sorry it took a long time to get this chapter out. I've been busy with my other stories. Anyway, review and I'll post the bonus chapter.**


	9. Bonus Chapter

**Bonus Chapter: Saving the Twins**

_On "Lyoko"_

_Aelita's POV_

I was with Christopher in the tower, wondering what was taking them so long to get us home. "How long has it been?" I asked him. "According to Dad, three months." He said. I was completely flabbergasted. "What all have they been doing?" I asked. "Calm down, sis. I'm sure they're working as hard as they can." He told me. I calmed down and went back to meditating when I saw him do it.

_In the lab_

_General POV_

"Any progress?" Alice asked the five geniuses in the lab. "Very little." Jeremie said. Alice had a sad look on her face. She looked over to Christopher and a tear fell from her eye. "Can't we try an old program that used to be in their father's supercomputer?" Alice asked, as Jeremie suddenly had an idea. "Yes, yes we can." Jeremie said excitedly as he ran to the helmet that the team had been using to contact the twins locked in limbo.

_On "Lyoko"_

_Christopher's POV_

Aelita and I were meditating when we heard from the lab. "Chris! Aelita!" Jeremie said, making us jump a little. "Warn us next time, Einstein." I said. "Seriously." Aelita said. "Sorry guys. Anyway, you guys remember that old materialization program that we used for you both?" He asked us. "You mean Code: Earth?" Aelita asked. "Yeah." Jeremie replied. "Yeah. What about it?" I asked. "Do you think we could try using it to bring you guys home?" Jeremie asked, and we realized what he meant when he brought up the subject. "It's worth a try." Aelita said, earning support from me. "Try to find the file." I ordered. "How?" He asked me. "Go up to my room, and look in the place I found my necklace. In the box, you'll find a data chip with all of the files from the supercomputer on it. Bring the chip back to the lab and plug it into the mainframe. It'll be on a highly restricted file. Once it's connected, place the helmet on, and I'll tell you the passcode you'll need to access it. I'll guide you from there." Christopher instructed.

_On Earth_

_Jeremie's POV_

I took the helmet off and told the others in the lab that they said it was worth a try. I then ran to Christopher's bedroom, went to where he told me it was when we were still in school, pulled the picture down from the wall, pulled the chip from the box and ran to the elevator when the others looked curious as to why I dashed to Christopher's room and back. "Guys, I think I might found a way to bring our elvish twins home." I said before explaining Christopher's instructions. I plugged the chip into the lab computer's mainframe, and placed the helmet back on and told him I was ready. "Okay Jeremie. Now, go to where it says highly restricted and type in the code SCIPIO. Then go under the file name BTE, which stands for Back To Earth. That's the Code: Earth program. Run it and we'll hope it works." Christopher instructed. Jeremie followed his friend's instructions to the letter. And within a few hours, the Schaeffer twins managed to return to their bodies, with the others in the lab cheering as Christopher and Aelita used their Energy Fields to break free from the capsules. Now, the heroes could celebrate by their friends' return back home.

**That's the story. I hope you guys enjoy this story. Review and ill make more stories.**


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